Randy-
I'm lucky to live/build in an area where the relative humidity doesn't vary much throughout the year (around 50%) so there's not a lot of wood movement during a build.
One thing about problems at the ends of a kayak - everything you do to the inside will be completely hidden, so cosmetics don't really matter. As long as you don't leave any sharp fiberglass shards sticking out to puncture your dry bags later....

I'd consider removing the glass from the inside of the hull at the ends where you need to make things more flexible, and re-glassing with the correct shape set by temporary struts/spacers.
If necessary, you could even laminate up a couple of lightweight 'deck beams' to bond in place before you add the deck.